It is possible there was an issue with a scan file, or one of the daemons is hung. Here is a simple way to reset the inventory on the 64 bit linux agent. This does require alternate credentials to be set in the Scheduler Service as it utilizes the agent push functionality.
1- Create a Linux Agent named "ResetLinuxInventory"
2- Save the agent
3- Open the ldlogon folder
4- Locate ResetLinuxInventory.sh
5- Right click on the file and select "Edit"
6- Remove the contents of the file and replace with:
#!/bin/bash
pkill map-*
service map-scraper stop
service map-scheduler stop
rm -rf /opt/landesk/jobs/filescan*
rm -rf /opt/landesk/jobs/map-scraper*
rm -rf /opt/landesk/jobs/scanner*
rm -rf /opt/landesk/scan_repository/*.*
service map-scraper start
service map-scheduler start
/opt/landesk/bin/ldiscan
7- Save and close file
8- Right click the ResetLinuxInventory.sh and select properties
9- select "Read Only" and click OK
10- Schedule the agent for deployment
11- add Linux machines that have not checked in inventory
12- Start task